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Port details
plink 1.07_3 biology on this many watch lists=0 search for ports that depend on this port
Whole genome association analysis toolset
Maintained by: jwbacon@tds.net search for ports maintained by this maintainer
Port Added: 27 Sep 2012 10:00:09
Also Listed In: science
License: GPLv2


PLINK is a free, open-source whole genome association analysis toolset,
designed to perform a range of basic, large-scale analyses in a
computationally efficient manner.

WWW: http://pngu.mgh.harvard.edu/~purcell/plink/
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.

Required To Build:
  1. lang/gcc
  2. devel/gmake
  3. devel/binutils
Required To Run:
  1. lang/gcc
Required Libraries:
  1. math/lapack
There are no ports dependent upon this port

To install the port: cd /usr/ports/biology/plink/ && make install clean
To add the package: pkg install biology/plink


Configuration Options
     No options to configure

Master Sites:
  1. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/
  2. http://pngu.mgh.harvard.edu/~purcell/plink/dist/

Number of commits found: 8

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
10 Mar 2014 20:55:22
Original commit files touched by this commit  1.07_3
Revision:347809
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
07 Mar 2014 15:52:40
Original commit files touched by this commit  1.07_2
Revision:347402
bapt search for other commits by this committer
Convert b* to USES=zip
16 Feb 2014 17:15:32
Original commit files touched by this commit  1.07_2
Revision:344614
tijl search for other commits by this committer
Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes".  In most cases
USE_GCC=yes has been omitted though.

Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.

Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...

Exp-run:	bdrewery
Approved by:	portmgr (bdrewery)
13 Dec 2013 09:34:40
Original commit files touched by this commit  1.07_1
Revision:336328
gerald search for other commits by this committer
Fix the build with more standards-compliant compilers such as GCC 4.7. [1]

On the way replace USE_GMAKE by USES=gmake.

PR:		184566 [1], 182136
Submitted by:	Christoph Moench-Tegeder <cmt@burggraben.net> [1]
Approved by:	maintainer (Jason Bacon <jwbacon@tds.net>) [1]
11 Dec 2013 14:43:51
Original commit files touched by this commit  1.07_1
Revision:336171
bapt search for other commits by this committer
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
26 Oct 2013 00:52:36
Original commit files touched by this commit  1.07_1
Revision:331644
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above View all of this commit message)
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.07
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
27 Sep 2012 09:59:25
Original commit files touched by this commit  1.07
Revision:304954
makc search for other commits by this committer
Add new ports biology/plink [1] and biology/plinkseq [2]:

PLINK is a free, open-source whole genome association analysis toolset.
PLINK/SEQ is an open-source C/C++ library for working with human
genetic variation data.

PR:		ports/171918 [1]
PR:		ports/171922 [2]
Submitted by:	Jason Bacon <jwbacon at tds.net>

Number of commits found: 8

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